ITS and 16S bioinformatic pipiliens to run on HPCC at Michigan State University.
Tools used:
USEARCH, avilable here https://www.drive5.com/usearch/
VSEARCH https://github.com/torognes/vsearch
QIIME https://github.com/Gian77/qiime
FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Spades http://bioinf.spbau.ru/spades
cutadapt http://cutadapt.readthedocs.io/en/stable/guide.html
seqtk https://github.com/lh3/seqtk
bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
CONSTAX https://github.com/natalie-vandepol/compare_taxonomy
RDP https://github.com/rdpstaff/classifier
Taxonomic References Databases:
UNITE https://unite.ut.ee/
GREENGENES http://greengenes.lbl.gov/Download/
SILVA https://www.arb-silva.de/